Supplementary Figure 5: General scheme of MD simulation and the structural models.
From: Structural basis of lipid-driven conformational transitions in the KvAP voltage-sensing domain
(a) Simple representation of the pseudo-spin (EP1, EP2 and EP3) exposure to different environments in a membrane protein. (b) schematic representation of a protein attached with the HO-1944 cross-linked nitroxide spin label which transforms into a simple pseudoatom (EPX) representation. EPX is covalently attached to the backbone Cαi and Cαi +3 (or Cαi +4). (c) The ten EPX-EPX distance restraints used for restrained molecular dynamics calculation. (d) During the RMD run, distance and accessibility (PaDSAR method) restraints were imposed. (e) Superimposition of crystal structure (PDB 1ORS) (yellow) and the simulated Up state model (blue). (f) Top: the best ten structures of Down state (red) models was superimposed with Up state model (blue). Bottom: structure comparison between the two average models representing the up (blue) and down (red) conformations.
